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Export SMARTS [message #2402]

Fri, 21 March 2025 04:30

zhentg
Messages: 32
Registered: March 2020

Member

DW structure sketcher is powerful for query definition, can the query be export as SMARTS?

Datawarrior is a good tool

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Re: Export SMARTS [message #2403 is a reply to message #2402]

Sat, 22 March 2025 16:40

nbehrnd
Messages: 233
Registered: June 2019

Senior Member

Hello zhentg,

as a side note, Noel O'Boyle published a two-part «Smarts for Dummies» blog post including a link to interactively test bench "Smarter SMARTS". Though JavaScript (the eventual/current language of implementation) isn't Java used by DataWarrior, I speculate a similar «preview» were a nice complementary addition to DataWarrior.

Best regards,

Norwid

https://baoilleach.blogspot.com/2018/11/smarts-for-dummies.h tml
https://baoilleach.blogspot.com/2023/02/smarts-for-dummies-p art-ii.html
https://baoilleach.github.io/smartersmarts-js/

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Re: Export SMARTS [message #2406 is a reply to message #2403]

Mon, 24 March 2025 16:02

zhentg
Messages: 32
Registered: March 2020

Member

Hi Norwid, thanks for providing the links, they are helpful.

https://smarts.plus/smartsview is a good tool to visualize SMARTS, but it does not provide examples that my SMARTS will match.

Datawarrior is a good tool

[Updated on: Mon, 24 March 2025 16:06]

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Re: Export SMARTS [message #2409 is a reply to message #2406]

Fri, 04 April 2025 21:11

thomas
Messages: 730
Registered: June 2014

Senior Member

DataWarrior's structure definitions with query features and exclude groups (OpenChemLib functionality) and the query features that can be encoded in SMARTS are partially overlapping and similar, but not really equivalent. And, although, recursive SMARTS and of DataWarrior's exclude groups are used for similar purposes, their concepts are substantially different. Stereochemistry in SMILES and SMARTS is simpler and the aromaticity concept is different. Therefore, direct translation is impossible. DataWarrior does its best to convert back and forth between SMARTS and DataWarrior substructures, but often some features cannot be interpreted one-to-one. Thus, when you are looking for a SMARTS editor I also suggest looking somewhere else, e.g. RD-Kit or at Matthias Rarey's excellent pattern editor: https://www.zbh.uni-hamburg.de/forschung/amd/software/smarts editor/smartseditor-doku.html

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Re: Export SMARTS [message #2410 is a reply to message #2409]

Sun, 06 April 2025 13:02

zhentg
Messages: 32
Registered: March 2020

Member

Thanks, Thomas. I did try SMARTSEditor, and it is useful.
Now I acknowledged that the syntax used in DW is not the same as SMARTS, thanks for providing details about this.

Datawarrior is a good tool

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